beta-Barrel membrane bacterial proteins: structure, function, assembly and interaction with lipids

Membrane proteins, although constituting about one-third of all proteins encoded by the genomes of living organisms, are still strongly underrepresented in the database of 3D protein structures, which reflects the big challenge presented by this class of proteins. Structural biologists, by employing electron and x-ray approaches, are continuously revealing new and fundamental insights into the structure, function, assembly and interaction with lipids of membrane proteins. To date, two structural motifs, alpha-helices and beta-sheets, have been found in membrane proteins and interestingly these two structural motives correlate with the location: while alpha-helical bundles are most often found in the receptors and ion channels of plasma and endoplasmic reticulum membranes, beta-barrels are restricted to the outer membrane of Gram-negative bacteria and in the mitochondrial membrane, and represent the structural motif used by several microbial toxins to form cytotoxic transmembrane channels. The beta-barrel, while being a rigid and stable motif is a versatile scaffold, having a wide variation in the size of the barrel, in the mechanism to open or close the gate and to impose selectivity on substrates. Even if the number of x-ray structures of integral membrane proteins has greatly increased in recent years, only a few of them provide information at a molecular level on how proteins interact with lipids that surround them in the membrane. The detailed mechanism of protein lipid interactions is of fundamental importance for understanding membrane protein folding, membrane adsorption, insertion and function in lipid bilayers. Both specific and unspecific interactions with lipids may participate in protein folding and assembly.     

Pervaporation from a dense membrane: roles of permeant-membrane interactions, Kelvin effect, and membrane swelling

Dense polymeric membranes with extremely small pores in the form of free volume are used widely in the pervaporative separation of liquid mixtures. The membrane permeation of a component followed by its vaporization on the opposite face is governed by the solubility and downstream pressure. We measured the evaporative flux of pure methanol and 2-propanol using dense membranes with different free volumes and different affinities (wettabilities and solubilities) for the permeant. Interestingly, the evaporative flux for different membranes vanished substantially (10-75%) below the equilibrium vapor pressure in the bulk. The discrepancy was larger for a smaller pore size and for more wettable membranes (higher positive spreading coefficients). This observation, which cannot be explained by the existing (mostly solution-diffusion type) models ofpervaporation, suggests an important role for the membrane-permeant interactions in nanopores that can lower the equilibrium vapor pressure. The pore sizes, as estimated from the positron annihilation, ranged from 0.2 to 0.6 nm for the dry membranes. Solubilities of methanol in different composite membranes were estimated from the Flory-Huggins theory. The interaction parameter was obtained from the surface properties measured by the contact angle goniometry in conjunction with the acid-base theory of polar surface interactions. For the membranes examined, the increase in the "wet" pore volume due to membrane swelling correlates almost linearly with the solubility of methanol in these membranes. Indeed, the observations are found to be consistent with the lowering of the equilibrium vapor pressure on the basis of the Kelvin equation. Thus, a higher solubility or selectivity of a membrane also implies stronger permeant-membrane interactions and a greater retention of the permeant by the membrane, thus decreasing its evaporative flux. This observation has important implications for the interpretation of existing experiments and in the separation of liquid mixtures by pervaporation.     

Chemically bound gold nanoparticle arrays on silicon: assembly, properties and SERS study of protein interactions

A highly reproducible and facile method for formation of ordered 2 dimensional arrays of CTAB protected 50 nm gold nanoparticles bonded to silicon wafers is described. The silicon wafers have been chemically modified with long-chain silanes terminated with thiol that penetrate the CTAB bilayer and chemically bind to the underlying gold nanoparticle. The silicon wafer provides a reproducibly smooth, chemically functionalizable and non-fluorescent substrate with a silicon phonon mode which may provide a convenient internal frequency and intensity calibration for vibrational spectroscopy. The CTAB bilayer provides a potentially biomimetic environment for analyte, yet allows a sufficiently small nanoparticle separation to achieve a significant electric field enhancement. The arrays have been characterized using SEM and Raman spectroscopy. These studies reveal that the reproducibility of the arrays is excellent both between batches (<10% RSD) and across a single batch (<5% RSD). The arrays also exhibit good stability, and the effect of temperature on the arrays was also investigated. The interaction of protein and amino acid with the nanoparticle arrays was investigated using Raman microscopy to investigate their potential in bio-SERS spectroscopy. Raman of phenylalanine and the protein bovine pancreatic trypsin inhibitor, BPTI were studied using 785 nm excitation, coincident with the surface plasmon absorbance of the array. The arrays exhibit SERS enhancements of the order of 2.6 x 10(4) for phenylalanine, the standard deviation on the relative intensity of the 1555 cm(-1) mode of phenylalanine is less than 10% for 100 randomly distributed locations across a single substrate and less than 20% between different substrates. Significantly, comparisons of the Raman spectra of the protein and phenylalanine in solution and immobilized on the nanoparticle arrays indicates that the protein is non-randomly orientated on the arrays. Selective SERS enhancements suggest that aromatic residues penetrate through the bilayer inducing conformational changes in the protein.     

A thiazole-containing tripodal ligand: synthesis, characterization, and interactions with metal ions and matrix metalloproteinases

A new tripodal ligand, tris[2-(((2-thiazolyl)methylidene)amino)ethyl]amine (Tatren), has been synthesized and characterized by NMR, IR, and UV-visible absorbance spectroscopy and elemental analysis. Tatren forms stable complexes with transition metal ions (Zn(2+), 1; Mn(2+), 2; Co(2+), 3) and the alkaline earth metal ions (Ca(2+), 4; Mg(2+), 5). Single-crystal X-ray structures of 1, 2, and 5 revealed six-coordinate chelate complexes with formula [M(Tatren)](ClO(4))(2) in which the metal centers are coordinated by three thiazolyl N atoms and three acyclic imine N atoms. Crystals of 1, 2, and 5 are monoclinic, P2(1)/c space group. Crystals of 4 are triclinic, P space group. The Ca(2+) complex is eight-coordinate with all N atoms of Tatren and one water molecule coordinated to the metal ion. Spectrophotometric titrations show that formation constants for the chelates of metal ions are >1 in methanol. Free Tatren inhibits the catalytic domain of matrix metalloproteinase-13 (MMP-13, collagenase-3) with K(i) = 3.5 +/- 0.6 microM. Molecular mechanics-based docking calculations suggest that one leg of Tatren coordinates to the catalytic Zn(2+) in MMPs-2, -9, and -13 with significant hydrogen bonding to backbone amide groups. High-level DFT calculations suggest that, in the absence of nonbonded interactions between Tatren and the enzyme, the most stable first coordination sphere of the catalytic Zn(2+) is achieved with three imidazolyl groups from His residues and two imine N atoms from one leg of Tatren. While complexes (1-3) do not inhibit MMP-13 to a significant extent, 4 does (K(i) = 30 +/- 10 microM). Hence, this study shows that tripodal chelating ligands of this class and their Ca(2+) complexes have potential as active-site inhibitors for MMPs.     

Electrostatic interactions between double layers: influence of surface roughness, regulation, and chemical heterogeneities

Electrostatic interactions between two surfaces as measured by atomic force microscopy (AFM) are usually analyzed in terms of DLVO theory. The discrepancies often observed between the experimental and theoretical behavior are usually ascribed to the occurrence of chemical regulation processes and/or to the presence of surface chemical or morphological heterogeneities (roughness). In this paper, a two-gradient mean-field lattice analysis is elaborated to quantifying double layer interactions between nonplanar surfaces. It allows for the implementation of the aforementioned sources of deviation from DLVO predictions. Two types of ion-surface interaction ensure the adjustment of charges and potentials upon double layer overlap, i.e., specific ionic adsorption at the surfaces and/or the presence of charge-determining ions for the surfaces considered. Upon double layer overlap, charges and potentials are adjusted via reequilibrium of the different ion adsorption processes. Roughness is modeled by grafting asperities on supporting planar surfaces, with their respective positions, shapes, and chemical properties being assigned at will. Local potential and charge distributions are derived by numerically solving the nonlinear Poisson-Boltzmann equation under the boundary conditions imposed by the surface profiles and regulation mechanism chosen. Finite size of the ions is taken into account. A number of characteristic situations are briefly discussed. It is shown how the surface irregularities are reflected in the Gibbs energy of interaction.     

The influence of matrix concentration and solvent composition on the results of MALDI MSI,with the aid of wet-interface matrix deposition

Imaging mass spectrometry is a powerful technique for the molecular analysis of tissue sections. As in many analytical methods, sample preparation is one of the main and most important steps to obtain results of good quality. Usually, the matrix concentration and solvent composition in different studies are taken for granted without any further consideration. In our studies, we aimed to find how matrix concentration and a type of solvent influence the signal. Moreover, we also aimed to find the relationship between these parameters, how they influence the spectra, and how they influence obtained ion maps. In our experiments, we used SunCollect®, which is a commercially available wet-interface system for matrix deposition. We decided to choose two matrix concentrations (2,5-dihydroxybenzoic acid [DHB]: 15 and 25 mg/mL; 9-aminoacridine [9AA]: 7 and 5 mg/mL) and two different water solutions of solvents in two different percentages for the matrices (DHB: 50% and 70% of methanol [MeOH] and acetonitrile [ACN]; 9AA 70% and 50% of ethanol [EtOH] and MeOH). In the end, the influence of these parameters on obtained spectra and ion maps was assessed.     

Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation

We have previously demonstrated that non-self-associating protein building blocks can oligomerize to form discrete supramolecular assemblies under the control of metal coordination. We show here that secondary interactions (salt bridges and hydrogen bonds) can be critical in guiding the metal-induced self-assembly of proteins. Crystallographic and hydrodynamic measurements on appropriately engineered cytochrome cb562 variants pinpoint the importance of a single salt-bridging arginine side chain in determining whether the protein monomers form a discrete Zn-induced tetrameric complex or heterogeneous aggregates. The combined ability to direct PPIs through metal coordination and secondary interactions should provide the specificity required for the construction of complex protein superstructures and the selective control of cellular processes that involve protein-protein association reactions.     

Ceramic microsieves: influence of perforation shape and distribution on flow resistance and membrane strength

Ceramic microsieves with slit-shaped perforations were compared to sieves with circular-shaped perforations, regarding flow resistance and membrane strength. Destructive tests show that the highest strength is obtained if the perforations are placed in a non-alternating pattern. Especially for slits, alternating patterns should be avoided as they make the structure unnecessarily flexible. The highest stress occurs at the edges of the membrane where it is attached to the support. Flexible structures bend stronger and therefore cause a higher stress at the edge, resulting in an easier rupture of the membrane. Our results show that ceramic microsieves with slits show a four to five-fold decrease in flow resistance for comparable strength related to sieves with circular pores.     

Electrochemical characterization of an asymmetric nanofiltration membrane with NaCl and KCl solutions: influence of membrane asymmetry on transport parameters

Electrochemical characterization of a nanofiltration asymmetric membrane was carried out by measuring membrane potential, salt diffusion, and electrical parameters (membrane electrical resistance and capacitance) with the membrane in contact with NaCl and KCl solutions at different concentrations (10(-3)< or =c(M)< or =5 x 10(-2)). From these experiments characteristic parameters such as the effective concentration of charge in the membrane, ionic transport numbers, and salt and ionic permeabilities across the membrane were determined. Membrane electrical resistance and capacitance were obtained from impedance spectroscopy (IS) measurements by using equivalent circuits as models. This technique allows the determination of the electrical contribution associated with each sublayer; then, assuming that the dense sublayer behaves as a plane capacitor, its thickness can be estimated from the capacitance value. The influence of membrane asymmetry on transport parameters have been studied by carrying out measurements for the two opposite external conditions. Results show that membrane asymmetry strongly affects membrane potential, which is attributed to the Donnan exclusion when the solutions in contact with the dense layer have concentrations lower than the membrane fixed charge (X(ef) approximately -0.004 M), but for the reversal experimental condition (high concentration in contact with the membrane dense sublayer) the membrane potential is practically similar to the solution diffusion potential. The comparison of results obtained for both electrolytes agrees with the higher conductivity of KCl solutions. On the other hand, the influence of diffusion layers at the membrane/solution interfaces in salt permeation was also studied by measuring salt diffusion at a given NaCl concentration gradient but at five different solutions stirring rates.     

Dye removal using 4A-zeolite/polyvinyl alcohol mixed matrix membrane adsorbents: preparation,characterization, adsorption,kinetics, and thermodynamics

In pursuit of improving performance of the methylene blue adsorption process, the potential of a novel 4A-zeolite/polyvinyl alcohol (PVA) membrane adsorbent was investigated. Adding 4A-zeolite particles to the PVA membrane adsorbent provided an effective structure for the adsorptive membrane in dye removal processes. Effect of zeolite content was also studied via synthesis of different mixed matrix membrane adsorbents (MMMAs) with 5, 10, 15, and 20 wt% 4A-zeolite content. Morphology of MMMAs was analyzed by scanning electron microscope and the intermolecular interactions were determined by Fourier transform infrared spectroscopy. X-ray diffraction was performed to determine the crystal structure of MMMAs. For the sake of finding optimum condition, the adsorption capacity was examined at various operating parameters, such as contact time, temperature, pH, and initial concentration. The maximum value of the adsorption capacity (q _e) of 41.08 mg g^?1 and the highest removal efficiency of 87.41 % were obtained by applying 20 wt% loading of 4A-zeolite. The experimental data were fitted well with the Freundlich adsorption isotherm model (R ² = 0.9917) compared with the Langmuir (R ² = 0.9489) and the Tempkin (R ² = 0.8886) adsorption isotherm models, and the adsorption kinetic data verified the best fitting with the pseudo-second-order model (R ² = 0.9999). The estimated data for Gibb’s free energy (ΔG°) showed that the adsorption process is spontaneous at lower temperature values and non-spontaneous at higher temperature values. Other evaluated thermodynamic parameters such as changing in enthalpy (ΔH°) and entropy (ΔS°) revealed that the adsorption process is exothermic with an increase in orderliness at the solid/solution interface.     

Shell-crosslinked nanostructures from amphiphilic AB and ABA block copolymers of styrene-alt-(maleic anhydride) and styrene: polymerization, assembly and stabilization in one pot

Shell-crosslinked nanostructures having unusual rosette morphologies have been produced by a simple process from styrene and maleic anhydride.     

Facile synthesis,crystal growth,characterization and computational study of new pyridine-based halogenated hydrazones: Unveiling the stabilization behavior in terms of noncovalent interactions

The pyridine-based halogenated hydrazone derivatives (E)-N′-benzylidene-2-[(6″-chloroazin-2″-yl)oxy]acetohydrazide ( 6a ), (E)-N′-(3′-chlorobenzylidene)-2-[(6″-chloroazin-2″-yl)oxy]acetohydrazide ( 6b ) and (E)-N′-(3′-bromobenzylidene)-2-[(6″-chloroazin-2″-yl)oxy]acetohydrazide ( 6c ) have been obtained using 6-chloro-2-hydroxypyridine. The structure of the products ( 6a – c ) has been verified using X-ray crystallography and spectroscopic approaches. A single-crystal X-ray diffraction (SC-XRD) investigation showed that the structures are stabilized by intermolecular attractive forces. Additionally, density functional theory (DFT) has been adopted to explore the structural properties, vibrational spectra, noncovalent interactions and frontier molecular orbitals using the B3LYP/6-311 + G(d,p) level. The nonlinear optical properties of the title compounds were calculated using the CAM-B3LYP/6-311 + G(d,p) level. Frequency analysis confirmed the stability of the molecules, and an excellent correlation was observed between the DFT- and SC-XRD-based structural parameters. The SC-XRD analysis confirmed that the dimers of 6a , 6b and 6c are linked by hydrogen-bonding interactions. Natural bond orbital (NBO) analysis also reconfirmed the strength of intermolecular hydrogen-bonding and hyperconjugative interactions. NBO investigation was also utilized to analyze the atomic charges. Moreover, Fourier transform infrared and natural population analyses endorsed that there are significant N&bond;H⋅⋅⋅O&dbond;C hydrogen-bonding linkages in dimeric structures of the compounds. The hydrogen-bonding network and different sorts of hyperconjugative interactions are the main reasons for the stability of the products in the solid state. The highest occupied and lowest unoccupied molecular orbital energies and first-order nonlinear optical properties of these molecules are reported. The quantum chemical parameters were derived using frontier molecular orbital energies.     

Polysulfone-ZrO(2) surface interactions. The influence on formation, morphology and properties of zirfon-membranes

The interaction between polysulfone and ZrO(2) particles is studied as a function of the particle sintering temperature in order to understand the role of ZrO(2) on the formation, morphology, and properties of organo-mineral composite membranes. The adsorption between the sintered ZrO(2) and the constituents of polysulfone, 2,2-diphenylpropane and diphenyl sulfone, is investigated using high-pressure liquid chromatography. The influence of the polymer-ZrO(2) interaction on the flow behavior of the casting suspension is registered via viscoelastic measurements. The organo-mineral composite membranes are formed by immersion precipitation in water, and the resulting membrane morphology is analyzed using high-resolution SEM. The zirconia concentration in the top-layer of the composite structure is determined by XPS. Finally, the link between the polymer-filler interactions, the membrane formation process, and the resulting membrane structure and properties is established.     

Mixtures of charged colloid and neutral polymer: influence of electrostatic interactions on demixing and interfacial tension

The equilibrium phase behavior of a binary mixture of charged colloids and neutral, nonadsorbing polymers is studied within free-volume theory. A model mixture of charged hard-sphere macroions and ideal, coarse-grained, effective-sphere polymers is mapped first onto a binary hard-sphere mixture with nonadditive diameters and then onto an effective Asakura-Oosawa model [S. Asakura and F. Oosawa, J. Chem. Phys. 22, 1255 (1954)]. The effective model is defined by a single dimensionless parameter-the ratio of the polymer diameter to the effective colloid diameter. For high salt-to-counterion concentration ratios, a free-volume approximation for the free energy is used to compute the fluid phase diagram, which describes demixing into colloid-rich (liquid) and colloid-poor (vapor) phases. Increasing the range of electrostatic interactions shifts the demixing binodal toward higher polymer concentration, stabilizing the mixture. The enhanced stability is attributed to a weakening of polymer depletion-induced attraction between electrostatically repelling macroions. Comparison with predictions of density-functional theory reveals a corresponding increase in the liquid-vapor interfacial tension. The predicted trends in phase stability are consistent with observed behavior of protein-polysaccharide mixtures in food colloids.     

d-xylose-based bolaamphiphiles: Synthesis and influence of the spacer nature on their interfacial and membrane properties

A two-step synthesis, with good yields, of d-xylose-based bolaamphiphiles is described. The monolayer properties, the adsorption behavior and membrane destabilization properties of two bolaamphiphiles differing by their spacers (presence or absence of one double bond) were studied. The presence of one unsaturation has no influence on the interfacial organization at low compression but impairs the stability of the monolayer at high compression. Saturated and unsaturated molecules are suggested to adopt a loop structure at the interface at low compression. The higher degree of freedom of the saturated hydrophobic spacer does not affect the initial diffusion step of the bolaform from the subphase to the interface but greatly slows the arrangement step at the interface. However, once at the interface, their surface-active properties are similar. The higher flexibility of the saturated analogue spacer also greatly increases its lipid vesicle destabilizing property. Its rearrangement within the lipid bilayer is in favour of the formation of inverted phases, facilitating membrane fusion.     

Mercury-fluorine interactions: a matrix isolation investigation of Hg...F2, HgF2 and HgF4 in argon matrices

HgF(2) and Hg have been trapped in dilute F(2)/Ar and neat F(2) matrices, subjected to UV-Vis and vac-UV photolysis and annealing, with the products identified by FTIR, UV-Vis-NIR and Hg L(3)-edge XAFS spectroscopic techniques. Whilst there was no convincing evidence for the formation of HgF(4) under our argon matrix isolation conditions, a new Hg...F(2) complex was identified and subsequent photolysis yielded HgF(2) very cleanly. Hg L(3)-edge EXAFS has provided the first experimental value of 1.94(2) A for the Hg-F bond length in HgF(2), which is in excellent agreement with the computational values incorporating relativistic effects.     

Dielectric analysis of multi-layer structure of nanofiltration membrane in electrolyte solutions: Ion penetrability, selectivity, and influence of pH

A mathematical framework for analysing electrokinetic flow in microchannel networks is outlined. The model is based on conservation of volume and total charge at network junctions, but in contrast to earlier theories also incorporates conservation of ion charge there. The model is applied to mixed pressure-driven/electro-osmotic flows of binary electrolytes through homogeneous microchannels as well as a 4:1:4 contraction-expansion series network. Under conditions of specified volumetric flow rate and ion currents, non-linear steady-state phenomena may arise: when the direction of the net co-ion flux is opposite to the direction of the net volumetric flow, two different fully developed, steady-state flow solutions may be obtained. Model predictions are compared with two-dimensional computational fluid dynamics (CFD) simulations. For systems where two steady states are realisable, the ultimate steady behaviour is shown to depend in part upon the initial state of the system.     

Anion-selective membrane electrodes based on metalloporphyrins: The influence of lipophilic anionic and cationic sites on potentiometric selectivity

The role of lipophilic anionic and cationic additives on the potentiometric anion selectivities of polymer membrane electrodes prepared with various metalloporphyrins as anion selective ionophores is examined. The presence of lipophilic anionic sites (e.g. tetraphenylborate derivatives) is shown to enhance the non-Hofmeister anion selectivities of membranes doped with In(III) and Sn(IV) porphyrins. In contrast, membranes containing Co(III) porphyrins require the addition of lipophilic cationic sites (e.g. tridodecylmethylammonium ions) in order to achieve optimal anion selectivity (for nitrite and thiocyanate) as well as rapid and reversible Nernstian response toward these anionic species. These experimental results coupled with appropriate theoretical models that predict the effect of lipophilic anion and cation sites on the selectivities of membranes doped with either neutral or charged carrier type ionophores may be used to determine the operative ionophore mechanism of each metalloporphyrin complex within the organic membrane phase.     

Stiff, and sticky in the right places: the dramatic influence of preorganizing guest binding sites on the hydrogen bond-directed assembly of rotaxanes.

Structural rigidity and the preorganization of thread binding sites are shown to have a major influence on template efficiency in the synthesis of hydrogen bond-assembled rotaxanes. Preorganization is so effective, in fact, that with good hydrogen bond acceptors (amides) a "world record" yield of 97% for a [2]rotaxane is obtained. The truly remarkable feature of this efficient template, however, is that it allows even poor hydrogen bond acceptors (esters) to be used to prepare hydrogen bond-assembled rotaxanes, despite the presence of competing hydrogen bonding groups (anions) which bind the key intermediates at least 10000x more strongly than single, unorganized, ester groups! The structures of the rotaxanes are established unambiguously in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography. As a series they provide unique experimental information regarding the nature of amide-ester hydrogen bonding interactions; in particular they suggest that in CDCl(3), amide-ester NH...O=C hydrogen bonds are approximately 1 kcal mol(-)(1) weaker than the corresponding amide-amide interactions.